Why not just use the preexisting launcher reload system with some modifiers based on tech like reload level, feed system efficiency, and cargo handling multiplier.
Lets assume a missile load speed 10 times slower than launcher reload rate.
We'll look at a tier 2 destroyer from my last game.
Portland class Destroyer 9000 tons 256 Crew 1097.6 BP TCS 180 TH 500 EM 0
2777 km/s Armour 5-38 Shields 0-0 Sensors 1/1/0/0 Damage Control 2 PPV 42
Annual Failure Rate: 27% IFR: 0.4% Maintenance Capacity 191 MSP
Magazine 342 Spare Berths 7
10HS 100 EP Nuclear Pulse Engine (5) Power 100 Fuel Use 141.5% Armour 0 Exp 12%
Fuel Capacity 360,000 Litres Range 5.1 billion km (21 days at full power)
Size 6 Missile Launcher (R2) (7) Missile Size 6 Rate of Fire 90
Missile Fire Control 10/5 FC61-R120 (1) Range 61.6m km Resolution 120
Maverick Mk III (57) Speed: 13,800 km/s End: 84.2m Range: 69.7m km WH: 7 Size: 6 TH: 46 / 27 / 13
Active Search Sensor 10 /5 MR65-R120 (1) GPS 14400 Range 65.7m km Resolution 120
Missile to hit chances are vs targets moving at 3000 km/s, 5000 km/s and 10,000 km/s
This design is classed as a military vessel for maintenance purposes
Default reload rate is 90 for a size 6 missile, we'll assume it will take 900 seconds to load a single size 6 into the magazine, lets make this per cargo handling system on the ammunition ship, improved can load 2 in this time, advanced 4 in this time. Note that this is reload rate of 1, lets assume that increased launcher reload rate doesn't help magazine load speed, but magazine feed efficiency should however.
Magazine is about 1000 tons and holds 342 in total, that's 57 missiles at 900 seconds each so default reload time is 14.25 hours. Cargo handling systems weigh in at 100 tons a piece, it's not unreasonable to assume that an ammunition ship serving this 9000 ton ship will be of similar size, lets say we put 4 cargo handling system which is a mere 4% of the ship.
Load rate then is 3.56 hours. Which is significant, but compares to loading speed of other cargo, it will certainly prevent immediate reloads of a fleet during a battle, except in the case of box launchers which obviously can reload very fast by comparison. That time will be halved once improved handling is added, and of course if you have multiple ammo ships in the fleet you get improved transfer speed.
Next there magazine feed efficiency, what about each level reducing the speed penalty compared to normal launcher speed, research reducing load rate from 10 times down by 1 per level, the final feed efficiency tech drops it down to merely double.
So by top tech tier loading a size 6 missile would take only 180 seconds, you can load 4 per advanced cargo handling system, the hypothetical ammo tender we had above would reload the destroyer in only 10.6 minutes.
Without going to that extreme lets just assume we increase cargo handling systems to 6, and have researched improved cargo handling (10,000 points) and feed efficiency 80 and 85% (6000 points total).
Load time per size 6 missile becomes 720 seconds, thats 11 hours, divided by 12 for the 6 improved handling systems makes reloading the ship only take 57 minutes.
How does this sound?
Edit: I like the maintenance changes, my last game I placed a single maintenance colony in Barnards star which required either frequent mineral shipments, or mines on 5 movies in the system and even still needed shipping in uridium and neutronium.